HEADER HYDROLASE 30-JUN-16 5LF8 TITLE HUMAN NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 17 (NUDT17) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 17; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUDIX MOTIF 17; COMPND 5 EC: 3.6.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NUDT17; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS HYDROLASE, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC EXPDTA X-RAY DIFFRACTION AUTHOR S.MATHEA,C.TALLANT,E.SALAH,D.WANG,S.VELUPILLAI,R.NOWAK,S.OERUM, AUTHOR 2 T.KROJER,N.BURGESS-BROWN,F.VON DELFT,C.H.ARROWSMITH,A.M.EDWARDS, AUTHOR 3 C.BOUNTRA,K.HUBER,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 1 16-AUG-17 5LF8 0 JRNL AUTH K.HUBER JRNL TITL HUMAN NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 17 JRNL TITL 2 (NUDT17) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 11183 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 621 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.56 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 826 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.4420 REMARK 3 BIN FREE R VALUE SET COUNT : 41 REMARK 3 BIN FREE R VALUE : 0.4650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1770 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.26000 REMARK 3 B22 (A**2) : -3.26000 REMARK 3 B33 (A**2) : 10.56000 REMARK 3 B12 (A**2) : -1.63000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.392 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.310 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.305 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.873 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1822 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1670 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2503 ; 1.617 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3794 ; 0.989 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 246 ; 8.056 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 49 ;35.852 ;22.245 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 220 ;15.320 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;15.109 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 305 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2033 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 374 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1005 ; 5.799 ; 7.569 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1004 ; 5.800 ; 7.569 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1244 ; 8.540 ;11.329 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1245 ; 8.538 ;11.329 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 817 ; 5.451 ; 7.631 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 817 ; 5.429 ; 7.630 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1260 ; 7.964 ;11.369 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1874 ;11.343 ;61.064 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1875 ;11.340 ;61.069 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5LF8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1200000641. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9900 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11806 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.560 REMARK 200 RESOLUTION RANGE LOW (A) : 75.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SPG PH 7.0 30% PEG1K, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 75.95650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.85351 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 27.16500 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 75.95650 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 43.85351 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 27.16500 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 75.95650 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 43.85351 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 27.16500 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 75.95650 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 43.85351 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 27.16500 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 75.95650 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 43.85351 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 27.16500 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 75.95650 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 43.85351 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 27.16500 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 87.70701 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 54.33000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 87.70701 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 54.33000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 87.70701 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 54.33000 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 87.70701 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 54.33000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 87.70701 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 54.33000 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 87.70701 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 54.33000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLU A 3 REMARK 465 ALA A 29 REMARK 465 GLY A 30 REMARK 465 PRO A 31 REMARK 465 GLY A 32 REMARK 465 ARG A 44 REMARK 465 GLY A 45 REMARK 465 GLU A 76 REMARK 465 ARG A 77 REMARK 465 PRO A 78 REMARK 465 ARG A 79 REMARK 465 VAL A 80 REMARK 465 PRO A 81 REMARK 465 GLY A 82 REMARK 465 ALA A 83 REMARK 465 GLU A 84 REMARK 465 LEU A 85 REMARK 465 PRO A 86 REMARK 465 ALA A 225 REMARK 465 GLU A 226 REMARK 465 ASP A 227 REMARK 465 GLY A 228 REMARK 465 THR A 229 REMARK 465 GLU A 230 REMARK 465 THR A 231 REMARK 465 PRO A 232 REMARK 465 GLY A 233 REMARK 465 LEU A 234 REMARK 465 PRO A 240 REMARK 465 LEU A 244 REMARK 465 ALA A 245 REMARK 465 VAL A 246 REMARK 465 GLU A 247 REMARK 465 LEU A 248 REMARK 465 GLU A 249 REMARK 465 GLU A 250 REMARK 465 ASP A 251 REMARK 465 GLY A 252 REMARK 465 GLY A 294 REMARK 465 ARG A 295 REMARK 465 THR A 296 REMARK 465 PRO A 297 REMARK 465 PRO A 298 REMARK 465 PRO A 299 REMARK 465 CYS A 300 REMARK 465 LYS A 301 REMARK 465 SER A 302 REMARK 465 ALA A 303 REMARK 465 ALA A 304 REMARK 465 TYR A 305 REMARK 465 LEU A 306 REMARK 465 ASP A 307 REMARK 465 PRO A 308 REMARK 465 GLY A 309 REMARK 465 PRO A 310 REMARK 465 ALA A 311 REMARK 465 LYS A 312 REMARK 465 GLU A 313 REMARK 465 GLU A 314 REMARK 465 TRP A 315 REMARK 465 ASN A 316 REMARK 465 MET A 317 REMARK 465 ASP A 318 REMARK 465 PRO A 319 REMARK 465 LEU A 320 REMARK 465 PRO A 321 REMARK 465 PRO A 322 REMARK 465 ASN A 323 REMARK 465 GLN A 324 REMARK 465 GLY A 325 REMARK 465 SER A 326 REMARK 465 GLY A 327 REMARK 465 LYS A 328 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 5 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 9 CG CD1 CD2 REMARK 470 ARG A 13 CG CD NE CZ NH1 NH2 REMARK 470 SER A 16 OG REMARK 470 SER A 18 OG REMARK 470 ARG A 21 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 33 CG CD1 CD2 REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 ARG A 46 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 52 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 60 CD NE CZ NH1 NH2 REMARK 470 GLU A 75 CG CD OE1 OE2 REMARK 470 ASP A 88 CG OD1 OD2 REMARK 470 ARG A 89 CD NE CZ NH1 NH2 REMARK 470 SER A 102 OG REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 ARG A 113 CG CD NE CZ NH1 NH2 REMARK 470 THR A 114 OG1 CG2 REMARK 470 LEU A 115 CG CD1 CD2 REMARK 470 SER A 116 OG REMARK 470 VAL A 117 CG1 CG2 REMARK 470 SER A 118 OG REMARK 470 HIS A 128 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 131 CG CD1 CD2 REMARK 470 GLU A 132 CG CD OE1 OE2 REMARK 470 LEU A 135 CG CD1 CD2 REMARK 470 LEU A 140 CG CD1 CD2 REMARK 470 GLN A 153 CG CD OE1 NE2 REMARK 470 GLN A 155 CG CD OE1 NE2 REMARK 470 TYR A 168 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 172 CG CD1 CD2 REMARK 470 SER A 173 OG REMARK 470 LEU A 176 CG CD1 CD2 REMARK 470 LYS A 178 CG CD CE NZ REMARK 470 TYR A 179 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 191 CG CD OE1 NE2 REMARK 470 SER A 193 OG REMARK 470 GLN A 195 CG CD OE1 NE2 REMARK 470 GLN A 196 CG CD OE1 NE2 REMARK 470 GLN A 198 CG CD OE1 NE2 REMARK 470 ILE A 201 CD1 REMARK 470 GLN A 202 CG CD OE1 NE2 REMARK 470 ASN A 206 CG OD1 ND2 REMARK 470 GLU A 207 CG CD OE1 OE2 REMARK 470 LEU A 235 CG CD1 CD2 REMARK 470 GLN A 237 CD OE1 NE2 REMARK 470 ASP A 238 CG OD1 OD2 REMARK 470 LEU A 239 CG CD1 CD2 REMARK 470 SER A 242 OG REMARK 470 VAL A 243 CG1 CG2 REMARK 470 ARG A 253 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 255 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 258 CG1 CG2 REMARK 470 LEU A 259 CG CD1 CD2 REMARK 470 HIS A 260 CG ND1 CD2 CE1 NE2 REMARK 470 SER A 262 OG REMARK 470 MET A 271 CG SD CE REMARK 470 GLU A 273 CG CD OE1 OE2 REMARK 470 ASP A 274 CG OD1 OD2 REMARK 470 LYS A 275 CG CD CE NZ REMARK 470 LYS A 287 CD CE NZ REMARK 470 GLN A 291 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 502 O HOH A 502 17675 0.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 11 -138.25 -89.21 REMARK 500 PHE A 19 -52.51 90.19 REMARK 500 ASP A 92 171.54 -59.39 REMARK 500 THR A 114 32.42 -58.73 REMARK 500 LEU A 115 176.77 71.61 REMARK 500 SER A 116 111.98 70.94 REMARK 500 VAL A 117 82.37 61.45 REMARK 500 SER A 118 50.70 70.70 REMARK 500 LEU A 131 113.15 135.33 REMARK 500 GLU A 132 -5.48 68.63 REMARK 500 SER A 173 -8.08 -48.88 REMARK 500 LYS A 178 -80.69 -80.41 REMARK 500 GLN A 202 79.37 -152.92 REMARK 500 ALA A 272 156.60 -34.90 REMARK 500 GLU A 273 135.88 166.98 REMARK 500 ASP A 274 47.18 -102.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 EMC A 403 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 EMC A 403 C1 160.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 EMC A 402 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 40 SG REMARK 620 2 EMC A 402 C1 138.1 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EMC A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EMC A 403 DBREF 5LF8 A 1 328 UNP P0C025 NUD17_HUMAN 1 328 SEQRES 1 A 328 MET ALA GLU VAL ARG VAL GLN LEU LEU LEU SER ARG ARG SEQRES 2 A 328 PRO GLU SER VAL SER PHE ALA ARG SER VAL CYS GLY LEU SEQRES 3 A 328 LEU GLY ALA GLY PRO GLY LEU GLY THR TRP PRO ILE HIS SEQRES 4 A 328 CYS SER LEU LYS ARG GLY ARG LEU VAL LEU SER SER ARG SEQRES 5 A 328 PRO PHE PRO GLY ALA SER ALA ARG LEU PRO LEU GLN ARG SEQRES 6 A 328 PRO PRO PHE CYS PRO PHE ALA ALA LEU GLU GLU ARG PRO SEQRES 7 A 328 ARG VAL PRO GLY ALA GLU LEU PRO THR ASP ARG GLY VAL SEQRES 8 A 328 ASP LEU GLY VAL ALA VAL ILE LEU GLN SER SER ASP LYS SEQRES 9 A 328 THR VAL LEU LEU THR ARG ARG ALA ARG THR LEU SER VAL SEQRES 10 A 328 SER PRO ASN LEU TRP VAL PRO PRO GLY GLY HIS VAL GLU SEQRES 11 A 328 LEU GLU GLU GLU LEU LEU ASP GLY GLY LEU ARG GLU LEU SEQRES 12 A 328 TRP GLU GLU SER GLY LEU HIS LEU PRO GLN GLY GLN PHE SEQRES 13 A 328 SER TRP VAL PRO LEU GLY LEU TRP GLU SER ALA TYR PRO SEQRES 14 A 328 PRO ARG LEU SER TRP GLY LEU PRO LYS TYR HIS HIS ILE SEQRES 15 A 328 VAL LEU TYR LEU LEU VAL ILE SER GLN GLU SER GLN GLN SEQRES 16 A 328 GLN LEU GLN ALA ARG ILE GLN PRO ASN PRO ASN GLU VAL SEQRES 17 A 328 SER ALA LEU MET TRP LEU THR PRO ASP VAL ALA ALA ALA SEQRES 18 A 328 VAL ALA ALA ALA GLU ASP GLY THR GLU THR PRO GLY LEU SEQRES 19 A 328 LEU PRO GLN ASP LEU PRO PRO SER VAL LEU ALA VAL GLU SEQRES 20 A 328 LEU GLU GLU ASP GLY ARG ALA ARG PRO LEU VAL LEU HIS SEQRES 21 A 328 MET SER THR LEU LEU ARG MET ILE PRO THR MET ALA GLU SEQRES 22 A 328 ASP LYS GLU ARG VAL SER THR GLY THR LYS PHE ALA LEU SEQRES 23 A 328 LYS LEU TRP LEU GLN HIS LEU GLY ARG THR PRO PRO PRO SEQRES 24 A 328 CYS LYS SER ALA ALA TYR LEU ASP PRO GLY PRO ALA LYS SEQRES 25 A 328 GLU GLU TRP ASN MET ASP PRO LEU PRO PRO ASN GLN GLY SEQRES 26 A 328 SER GLY LYS HET PO4 A 401 5 HET EMC A 402 3 HET EMC A 403 3 HETNAM PO4 PHOSPHATE ION HETNAM EMC ETHYL MERCURY ION FORMUL 2 PO4 O4 P 3- FORMUL 3 EMC 2(C2 H5 HG 1+) FORMUL 5 HOH *3(H2 O) HELIX 1 AA1 SER A 22 GLY A 28 1 7 HELIX 2 AA2 CYS A 69 GLU A 75 1 7 HELIX 3 AA3 GLU A 134 GLY A 148 1 15 HELIX 4 AA4 ARG A 171 GLY A 175 5 5 HELIX 5 AA5 SER A 193 ARG A 200 1 8 HELIX 6 AA6 THR A 215 ALA A 224 1 10 HELIX 7 AA7 MET A 261 LEU A 265 1 5 HELIX 8 AA8 SER A 279 LEU A 293 1 15 SHEET 1 AA1 9 GLU A 15 SER A 16 0 SHEET 2 AA1 9 VAL A 6 LEU A 8 -1 N LEU A 8 O GLU A 15 SHEET 3 AA1 9 LEU A 47 SER A 50 1 O LEU A 47 N GLN A 7 SHEET 4 AA1 9 GLY A 34 SER A 41 -1 N SER A 41 O VAL A 48 SHEET 5 AA1 9 ALA A 59 GLN A 64 -1 O LEU A 61 N ILE A 38 SHEET 6 AA1 9 PHE A 156 TYR A 168 1 O LEU A 163 N PRO A 62 SHEET 7 AA1 9 TYR A 179 SER A 190 -1 O LEU A 187 N VAL A 159 SHEET 8 AA1 9 ASP A 92 GLN A 100 1 N GLN A 100 O SER A 190 SHEET 9 AA1 9 GLY A 126 HIS A 128 -1 O GLY A 127 N VAL A 95 SHEET 1 AA2 4 VAL A 208 LEU A 214 0 SHEET 2 AA2 4 VAL A 106 ARG A 111 -1 N ARG A 110 O ALA A 210 SHEET 3 AA2 4 LEU A 121 VAL A 123 -1 O VAL A 123 N THR A 109 SHEET 4 AA2 4 ARG A 277 VAL A 278 1 O ARG A 277 N TRP A 122 SHEET 1 AA3 2 GLN A 237 ASP A 238 0 SHEET 2 AA3 2 LEU A 259 HIS A 260 -1 O LEU A 259 N ASP A 238 LINK SG CYS A 24 HG EMC A 403 1555 1555 2.76 LINK SG CYS A 40 HG EMC A 402 1555 1555 2.69 CISPEP 1 TRP A 36 PRO A 37 0 -11.80 CISPEP 2 TYR A 168 PRO A 169 0 -9.03 SITE 1 AC1 5 PHE A 68 PRO A 170 ARG A 277 SER A 279 SITE 2 AC1 5 THR A 280 SITE 1 AC2 1 CYS A 40 SITE 1 AC3 3 CYS A 24 GLY A 34 THR A 35 CRYST1 151.913 151.913 81.495 90.00 90.00 120.00 H 3 2 18 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006583 0.003801 0.000000 0.00000 SCALE2 0.000000 0.007601 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012271 0.00000